Contacts of the helix formed by residues 238 - 251 (chain C) in PDB entry 6ERH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C GLU* 4.0 15.3 - - - +
62C MET* 3.9 4.4 - - - +
237C SER* 1.3 93.8 + - - +
239C LEU* 1.3 65.5 + - - +
240C GLU* 4.4 9.0 - - + +
241C ASP* 3.2 34.7 + - - +
242C LEU* 3.2 12.5 + - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 4.4 4.4 + - - +
57C LEU* 4.6 11.7 - - + -
62C MET* 3.5 44.3 - - + +
65C GLN* 3.7 29.2 - - + +
66C CYS* 3.8 21.3 - - + +
69C SER* 5.9 0.9 - - - +
238C LYS* 1.3 70.5 - - - +
240C GLU* 1.3 57.9 + - + +
242C LEU* 3.2 5.2 + - + +
243C LEU* 2.8 45.6 + - + +
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LYS* 3.3 7.2 - - + -
239C LEU* 1.3 82.4 - - + +
241C ASP* 1.3 64.8 + - - +
243C LEU* 3.5 9.2 + - - +
244C ARG* 3.2 32.8 + - - +
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Residues in contact with ASP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C SER* 4.1 4.7 - - - +
237C SER* 4.8 3.3 + - - -
238C LYS* 3.2 38.1 + - - +
240C GLU* 1.3 75.8 - - - +
242C LEU* 1.4 65.6 + - - +
244C ARG* 2.8 36.4 + - - +
245C LYS* 3.0 46.2 + - - +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C MET* 3.8 36.6 - - + +
63C SER* 4.0 6.1 - - - +
66C CYS* 3.9 15.5 - - + -
169C PHE* 4.1 9.0 - - + -
203C MET* 4.0 27.8 - - + +
205C LEU* 3.8 30.7 - - + -
236C SER* 3.5 22.5 + - - +
238C LYS 3.2 8.4 + - - +
239C LEU* 3.2 9.7 + - - +
241C ASP* 1.4 74.4 - - - +
243C LEU* 1.3 55.9 + - - +
245C LYS* 3.5 2.3 + - + +
246C VAL* 3.0 36.4 + - + +
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C CYS* 4.0 16.3 - - - +
69C SER* 3.6 36.6 - - - +
70C VAL* 5.5 5.3 - - + +
73C SER* 5.9 2.7 - - - +
239C LEU* 2.8 34.5 + - + +
240C GLU* 3.5 9.2 - - - +
241C ASP 3.2 0.2 - - - -
242C LEU* 1.3 75.9 - - - +
244C ARG* 1.3 58.8 + - + +
246C VAL* 3.3 2.9 + - - +
247C ARG* 2.9 43.7 + - + +
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Residues in contact with ARG 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C GLU* 3.2 20.7 + - - +
241C ASP* 2.8 31.8 + - - +
243C LEU* 1.3 77.3 - - + +
245C LYS* 1.3 55.7 + - + +
247C ARG* 3.4 5.6 + - - +
248C ALA* 2.8 37.9 + - - +
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Residues in contact with LYS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C MET* 4.1 12.8 - - - +
233C PHE* 3.6 48.4 - - + -
234C GLU* 2.8 31.0 + - - +
235C GLU 3.2 13.9 + - - -
236C SER* 2.8 29.9 + - - +
241C ASP* 3.0 28.5 + - - +
242C LEU* 3.7 4.5 - - + +
244C ARG* 1.3 75.2 - - + +
246C VAL* 1.3 63.0 + - - +
248C ALA* 3.5 4.5 + - - +
249C LYS* 3.4 18.5 + - - +
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 4.3 9.4 - - + -
66C CYS* 3.7 10.3 - - - -
70C VAL* 3.9 24.9 - - + -
167C MET* 3.7 17.7 - - - +
169C PHE* 3.6 28.0 - - + -
203C MET* 3.7 22.4 - - + -
242C LEU* 3.0 22.9 + - + +
243C LEU 3.7 3.4 - - - +
245C LYS* 1.3 72.9 - - - +
247C ARG* 1.3 61.2 + - - +
249C LYS* 3.2 5.2 + - - +
250C GLU* 2.9 31.0 + - + +
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Residues in contact with ARG 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C VAL* 4.6 12.5 - - + +
73C SER* 4.6 21.9 + - - -
74C LYS* 3.6 20.0 - - - +
77C SER* 4.4 17.2 + - - -
79C ASP* 4.9 3.2 + - - -
243C LEU* 2.9 32.6 + - + +
244C ARG* 4.0 4.9 - - - +
246C VAL* 1.3 74.6 - - + +
248C ALA* 1.4 59.6 + - - +
250C GLU* 2.8 34.1 + - - +
251C THR* 3.3 40.0 + - - +
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PHE* 4.5 14.1 - - + -
244C ARG 2.8 18.7 + - - +
245C LYS* 3.6 9.0 - - - +
247C ARG* 1.4 77.5 - - - +
249C LYS* 1.3 61.2 + - - +
251C THR 3.6 12.1 - - - +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ARG* 3.0 32.4 + - - +
167C MET* 4.0 6.5 - - + -
201C ASP* 3.4 41.6 + - - +
202C LEU 3.7 22.6 + - - +
203C MET* 3.7 11.9 - - + +
232C HIS* 4.0 18.4 + - - -
233C PHE* 3.7 30.6 - - + -
245C LYS 3.4 8.5 + - - +
246C VAL 3.2 6.7 + - - +
248C ALA* 1.3 74.1 - - - +
250C GLU* 1.3 62.5 + - - +
251C THR 4.3 1.9 - - - +
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.5 34.1 - - + +
70C VAL* 4.1 13.2 - - + -
74C LYS* 2.8 33.0 + - - -
81C ASP* 3.5 8.8 - - - +
165C ARG* 3.8 14.4 + - - +
167C MET* 4.5 2.6 - - + +
246C VAL* 2.9 19.6 + - + +
247C ARG* 2.8 40.5 + - - +
249C LYS* 1.3 79.2 - - - +
251C THR* 1.3 69.3 + - - +
252C ARG* 3.6 5.4 + - - +
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 4.7 1.3 + - - +
79C ASP* 5.2 7.4 - - - +
81C ASP* 6.0 0.4 - - - -
247C ARG* 3.3 35.8 + - - +
248C ALA 3.6 14.6 - - - +
249C LYS 4.3 1.7 - - - +
250C GLU* 1.3 93.7 + - - +
252C ARG* 1.3 74.3 + - - +
253C LYS* 4.2 0.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il